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I am getting an error while mapping the gene names to the StringDB identifiers using the map function. The code was working fine before with the StringDB version 11 but giving an error for version 11.5. Also, the StringDB version 11 is not accessible by the package.
string_db <- STRINGdb$new(version="11.5", species=9606,score_threshold=700, input_directory="")
geneMapped <- string_db$map(data.frame(gene=geneList), "gene", removeUnmappedRows = TRUE)
Error in `[.data.frame`(x, r, vars, drop = drop) :
undefined columns selected
sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] WGCNA_1.70-3 fastcluster_1.2.3 dynamicTreeCut_1.63-1 RSQLite_2.2.7 rDGIdb_1.16.0 openxlsx_4.2.4
[7] org.Hs.eg.db_3.12.0 AnnotationDbi_1.52.0 IRanges_2.24.1 S4Vectors_0.28.1 Biobase_2.50.0 BiocGenerics_0.36.1
[13] clusterProfiler_3.18.1 ReactomePA_1.34.0 influential_2.2.3 concaveman_1.1.0 ggforce_0.3.3 randomcoloR_1.1.0.1
[19] ggnewscale_0.4.5 ggnetwork_0.5.10 igraph_1.2.6 STRINGdb_2.2.2 plyr_1.8.6 stringr_1.4.0
[25] ggplot2_3.3.5 maftools_2.6.05
loaded via a namespace (and not attached):
[1] utf8_1.2.2 proto_1.0.0 tidyselect_1.1.1 htmlwidgets_1.5.3 grid_4.0.3
[6] BiocParallel_1.24.1 Rtsne_0.15 scatterpie_0.1.6 munsell_0.5.0 preprocessCore_1.52.1
[11] codetools_0.2-18 ragg_1.1.3 chron_2.3-56 withr_2.4.2 colorspace_2.0-2
[16] GOSemSim_2.16.1 knitr_1.33 rstudioapi_0.13 DOSE_3.16.0 labeling_0.4.2
[21] polyclip_1.10-0 bit64_4.0.5 farver_2.1.0 downloader_0.4 vctrs_0.3.8
[26] generics_0.1.0 xfun_0.24 BiocFileCache_1.14.0 R6_2.5.0 doParallel_1.0.16
[31] clue_0.3-59 graphlayouts_0.7.1 bitops_1.0-7 cachem_1.0.5 fgsea_1.16.0
[36] assertthat_0.2.1 promises_1.2.0.1 scales_1.1.1 vroom_1.5.3 nnet_7.3-16
[41] ggraph_2.0.5 enrichplot_1.10.2 gtable_0.3.0 Cairo_1.5-12.2 tidygraph_1.2.0
[46] rlang_0.4.11 systemfonts_1.0.2 GlobalOptions_0.1.2 splines_4.0.3 lazyeval_0.2.2
[51] impute_1.64.0 checkmate_2.0.0 BiocManager_1.30.16 yaml_2.2.1 reshape2_1.4.4
[56] backports_1.2.1 httpuv_1.6.1 Hmisc_4.5-0 qvalue_2.22.0 tools_4.0.3
[61] tcltk_4.0.3 ellipsis_0.3.2 gplots_3.1.1 RColorBrewer_1.1-2 gsubfn_0.7
[66] Rcpp_1.0.7 hash_2.2.6.1 base64enc_0.1-3 purrr_0.3.4 RCurl_1.98-1.3
[71] rpart_4.1-15 sqldf_0.4-11 GetoptLong_1.0.5 viridis_0.6.1 cowplot_1.1.1
[76] ggrepel_0.9.1 cluster_2.1.2 magrittr_2.0.1 data.table_1.14.0 DO.db_2.9
[81] circlize_0.4.13 reactome.db_1.74.0 matrixStats_0.60.0 hms_1.1.0 mime_0.11
[86] xtable_1.8-4 jpeg_0.1-9 gridExtra_2.3 shape_1.4.6 compiler_4.0.3
[91] tibble_3.1.3 KernSmooth_2.23-20 V8_3.4.2 crayon_1.4.1 shadowtext_0.0.8
[96] htmltools_0.5.1.1 later_1.2.0 tzdb_0.1.2 Formula_1.2-4 tidyr_1.1.3
[101] DBI_1.1.1 tweenr_1.0.2 ExperimentHub_1.16.1 dbplyr_2.1.1 ComplexHeatmap_2.6.2
[106] MASS_7.3-54 rappdirs_0.3.3 Matrix_1.3-4 readr_2.0.0 cli_3.0.1
[111] pkgconfig_2.0.3 rvcheck_0.1.8 foreign_0.8-81 plotly_4.9.4.1 foreach_1.5.1
[116] digest_0.6.27 graph_1.68.0 fastmatch_1.1-3 htmlTable_2.2.1 curl_4.3.2
[121] shiny_1.6.0 gtools_3.9.2 graphite_1.36.0 rjson_0.2.20 lifecycle_1.0.0
[126] jsonlite_1.7.2 viridisLite_0.4.0 fansi_0.5.0 pillar_1.6.2 lattice_0.20-44
[131] fastmap_1.1.0 httr_1.4.2 plotrix_3.8-1 survival_3.2-11 GO.db_3.12.1
[136] interactiveDisplayBase_1.28.0 glue_1.4.2 zip_2.2.0 png_0.1-7 iterators_1.0.13
[141] BiocVersion_3.12.0 bit_4.0.4 stringi_1.7.3 blob_1.2.2 textshaping_0.3.5
[146] AnnotationHub_2.22.1 latticeExtra_0.6-29 caTools_1.18.2 memoise_2.0.0 dplyr_1.0.7
Sorry for the late reply. The error should have been fixed by now.